Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

Abstract Background Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought s...

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Autores principales:	Ying Liang, Kunhua Wei, Fan Wei, Shuangshuang Qin, Chuanhua Deng, Yang Lin, Mingjie Li, Li Gu, Guili Wei, Jianhua Miao, Zhongyi Zhang
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Sophora tonkinensis Drought stress mRNA miRNA Next-generation sequencing Transcription factor Botany QK1-989
Acceso en línea:	https://doaj.org/article/562f7a6797d8480b81989db58335b224
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spelling	oai:doaj.org-article:562f7a6797d8480b81989db58335b2242021-12-05T12:06:17ZIntegrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis10.1186/s12870-021-03334-61471-2229https://doaj.org/article/562f7a6797d8480b81989db58335b2242021-12-01T00:00:00Zhttps://doi.org/10.1186/s12870-021-03334-6https://doaj.org/toc/1471-2229Abstract Background Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. Results To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. Conclusion This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.Ying LiangKunhua WeiFan WeiShuangshuang QinChuanhua DengYang LinMingjie LiLi GuGuili WeiJianhua MiaoZhongyi ZhangBMCarticleSophora tonkinensisDrought stressmRNAmiRNANext-generation sequencingTranscription factorBotanyQK1-989ENBMC Plant Biology, Vol 21, Iss 1, Pp 1-20 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Sophora tonkinensis Drought stress mRNA miRNA Next-generation sequencing Transcription factor Botany QK1-989
spellingShingle	Sophora tonkinensis Drought stress mRNA miRNA Next-generation sequencing Transcription factor Botany QK1-989 Ying Liang Kunhua Wei Fan Wei Shuangshuang Qin Chuanhua Deng Yang Lin Mingjie Li Li Gu Guili Wei Jianhua Miao Zhongyi Zhang Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis
description	Abstract Background Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. Results To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. Conclusion This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.
format	article
author	Ying Liang Kunhua Wei Fan Wei Shuangshuang Qin Chuanhua Deng Yang Lin Mingjie Li Li Gu Guili Wei Jianhua Miao Zhongyi Zhang
author_facet	Ying Liang Kunhua Wei Fan Wei Shuangshuang Qin Chuanhua Deng Yang Lin Mingjie Li Li Gu Guili Wei Jianhua Miao Zhongyi Zhang
author_sort	Ying Liang
title	Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis
title_short	Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis
title_full	Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis
title_fullStr	Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis
title_full_unstemmed	Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis
title_sort	integrated transcriptome and small rna sequencing analyses reveal a drought stress response network in sophora tonkinensis
publisher	BMC
publishDate	2021
url	https://doaj.org/article/562f7a6797d8480b81989db58335b224
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Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

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